The zooplankton community structure and diversity were analysed against the gradient of floodplain lakes connectivity and water level under different flood-pulse dynamics in the Vistula River. The lakes differed in terms of hydrology, among others in the degree/type of their connection with the river (permanent, temporary and no connection). The study was conducted during the growing seasons in the years 2006–2013 and involved the lower Vistula River and three floodplain lakes: isolated, transitional and connected. Water samples were collected biweekly from April to September. Zooplankton was the most diverse and abundant in the transitional lake (the highest Shannon α-diversity index H’ and Pielou’s evenness index J’). The gentle washing of the lakes might have stimulated the development of zooplankton in accordance with the Intermediate Disturbance Hypothesis. The diversity and density of zooplankton were higher in the connected lake compared to the isolated one. We confirmed the hypothesis that zooplankton should be more abundant and diverse in floodplain lakes connected with the river (or transitional) than in isolated ones. Zooplankton analyses indicated that hydrological conditions (flood-pulse regime) contributed most substantially to zooplankton diversity and density in the floodplain lakes of the lower Vistula valley.